FMO DATABASE

FMODB ID: ZY58N

Calculation Name: 1NYH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NYH

Chain ID: A

ChEMBL ID:

UniProt ID: P11978

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-326536.868393
FMO2-HF: Nuclear repulsion	296338.729021
FMO2-HF: Total energy	-30198.139372
FMO2-MP2: Total energy	-30285.138583

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1271:LEU)

Summations of interaction energy for fragment #1(A:1271:LEU)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-7.053	-0.599	2.02	-3.647	-4.828	-0.022

Interaction energy analysis for fragmet #1(A:1271:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : 0.012

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	1273	PHE	0	0.049	0.007	3.759	-2.120	0.059	-0.006	-1.163	-1.011	0.006
4	A	1274	VAL	0	0.005	0.004	6.192	0.490	0.490	0.000	0.000	0.000	0.000
5	A	1275	ASP	-1	-0.774	-0.909	2.604	-7.415	-3.791	1.914	-2.309	-3.229	-0.028
6	A	1276	ILE	0	-0.067	-0.009	2.793	0.105	0.756	0.112	-0.175	-0.588	0.000
7	A	1277	VAL	0	-0.006	-0.012	5.576	0.565	0.565	0.000	0.000	0.000	0.000
8	A	1278	LEU	0	0.035	0.015	7.815	0.239	0.239	0.000	0.000	0.000	0.000
9	A	1279	SER	0	-0.005	-0.001	6.102	0.365	0.365	0.000	0.000	0.000	0.000
10	A	1280	LYS	1	0.904	0.951	8.848	0.426	0.426	0.000	0.000	0.000	0.000
11	A	1281	ALA	0	0.009	0.013	11.179	0.093	0.093	0.000	0.000	0.000	0.000
12	A	1282	ALA	0	0.002	-0.007	11.730	0.064	0.064	0.000	0.000	0.000	0.000
13	A	1283	SER	0	-0.038	-0.024	12.450	0.074	0.074	0.000	0.000	0.000	0.000
14	A	1284	ALA	0	0.019	0.012	14.330	0.028	0.028	0.000	0.000	0.000	0.000
15	A	1285	LEU	0	-0.031	-0.010	16.900	0.024	0.024	0.000	0.000	0.000	0.000
16	A	1286	ASP	-1	-0.793	-0.886	16.728	0.045	0.045	0.000	0.000	0.000	0.000
17	A	1287	GLU	-1	-0.896	-0.951	16.373	-0.052	-0.052	0.000	0.000	0.000	0.000
18	A	1288	LYS	1	0.837	0.908	20.256	0.102	0.102	0.000	0.000	0.000	0.000
19	A	1289	GLU	-1	-0.878	-0.946	21.826	-0.058	-0.058	0.000	0.000	0.000	0.000
20	A	1290	LYS	1	0.833	0.905	19.287	-0.031	-0.031	0.000	0.000	0.000	0.000
21	A	1291	GLN	0	-0.014	-0.005	24.449	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	1292	LEU	0	0.011	0.016	26.520	0.004	0.004	0.000	0.000	0.000	0.000
23	A	1293	ALA	0	0.026	0.016	27.160	0.003	0.003	0.000	0.000	0.000	0.000
24	A	1294	VAL	0	-0.034	-0.017	28.415	0.004	0.004	0.000	0.000	0.000	0.000
25	A	1295	ALA	0	-0.009	-0.003	30.758	0.001	0.001	0.000	0.000	0.000	0.000
26	A	1296	ASN	0	-0.015	-0.027	31.105	0.001	0.001	0.000	0.000	0.000	0.000
27	A	1297	GLU	-1	-0.838	-0.869	33.410	0.012	0.012	0.000	0.000	0.000	0.000
28	A	1298	ILE	0	0.008	0.003	34.637	0.001	0.001	0.000	0.000	0.000	0.000
29	A	1299	ILE	0	0.012	0.012	35.743	0.000	0.000	0.000	0.000	0.000	0.000
30	A	1300	ARG	1	0.868	0.929	36.700	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	1301	SER	0	0.022	-0.011	39.163	0.001	0.001	0.000	0.000	0.000	0.000
32	A	1302	LEU	0	-0.018	-0.014	40.850	0.000	0.000	0.000	0.000	0.000	0.000
33	A	1303	SER	0	-0.020	-0.022	41.807	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	1304	ASP	-1	-0.844	-0.890	43.835	0.005	0.005	0.000	0.000	0.000	0.000
35	A	1305	GLU	-1	-0.957	-0.978	45.403	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	1306	VAL	0	-0.024	-0.011	46.788	0.000	0.000	0.000	0.000	0.000	0.000
37	A	1307	MET	0	0.052	0.027	47.288	0.001	0.001	0.000	0.000	0.000	0.000
38	A	1308	ARG	1	0.800	0.865	46.812	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	1309	ASN	0	-0.033	-0.016	50.202	0.001	0.001	0.000	0.000	0.000	0.000
40	A	1310	GLU	-1	-0.911	-0.947	52.674	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	1311	ILE	0	-0.014	0.004	53.567	0.000	0.000	0.000	0.000	0.000	0.000
42	A	1312	ARG	1	0.967	0.978	55.294	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	1313	ILE	0	-0.027	-0.016	56.560	0.000	0.000	0.000	0.000	0.000	0.000
44	A	1314	THR	0	0.023	0.004	58.723	0.000	0.000	0.000	0.000	0.000	0.000
45	A	1315	SER	0	-0.032	-0.007	60.510	0.000	0.000	0.000	0.000	0.000	0.000
46	A	1316	LEU	0	0.003	0.013	60.402	0.000	0.000	0.000	0.000	0.000	0.000
47	A	1317	GLN	0	-0.007	-0.001	62.663	0.000	0.000	0.000	0.000	0.000	0.000
48	A	1318	GLY	0	0.021	0.033	64.987	0.000	0.000	0.000	0.000	0.000	0.000
49	A	1319	ASP	-1	-0.865	-0.950	65.170	0.001	0.001	0.000	0.000	0.000	0.000
50	A	1320	LEU	0	-0.064	-0.031	67.553	0.000	0.000	0.000	0.000	0.000	0.000
51	A	1321	THR	0	-0.045	-0.049	68.781	0.000	0.000	0.000	0.000	0.000	0.000
52	A	1322	PHE	0	0.045	0.020	70.973	0.000	0.000	0.000	0.000	0.000	0.000
53	A	1323	THR	0	0.007	0.002	71.436	0.000	0.000	0.000	0.000	0.000	0.000
54	A	1324	LYS	1	0.965	0.983	71.118	0.004	0.004	0.000	0.000	0.000	0.000
55	A	1325	LYS	1	0.847	0.925	75.351	0.003	0.003	0.000	0.000	0.000	0.000
56	A	1326	CYS	0	-0.050	-0.024	76.247	0.000	0.000	0.000	0.000	0.000	0.000
57	A	1327	LEU	0	-0.023	-0.016	77.856	0.000	0.000	0.000	0.000	0.000	0.000
58	A	1328	GLU	-1	-0.840	-0.913	79.369	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	1329	ASN	0	0.010	0.000	81.325	0.000	0.000	0.000	0.000	0.000	0.000
60	A	1330	ALA	0	0.025	0.014	82.649	0.000	0.000	0.000	0.000	0.000	0.000
61	A	1331	ARG	1	0.907	0.946	82.409	0.002	0.002	0.000	0.000	0.000	0.000
62	A	1332	SER	0	0.028	0.027	85.278	0.000	0.000	0.000	0.000	0.000	0.000
63	A	1333	GLN	0	0.044	0.016	86.043	0.000	0.000	0.000	0.000	0.000	0.000
64	A	1334	ILE	0	-0.023	0.004	86.169	0.000	0.000	0.000	0.000	0.000	0.000
65	A	1335	SER	0	0.072	0.033	89.648	0.000	0.000	0.000	0.000	0.000	0.000
66	A	1336	GLU	-1	-0.958	-0.978	90.739	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	1337	LYS	1	0.809	0.890	90.664	0.000	0.000	0.000	0.000	0.000	0.000
68	A	1338	ASP	-1	-0.820	-0.909	92.749	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	1339	ALA	0	-0.026	-0.001	95.333	0.000	0.000	0.000	0.000	0.000	0.000
70	A	1340	LYS	1	0.897	0.928	97.719	0.000	0.000	0.000	0.000	0.000	0.000
71	A	1341	ILE	0	0.002	0.009	96.943	0.000	0.000	0.000	0.000	0.000	0.000
72	A	1342	ASN	0	-0.027	-0.037	97.887	0.000	0.000	0.000	0.000	0.000	0.000
73	A	1343	LYS	1	0.928	0.983	101.168	0.001	0.001	0.000	0.000	0.000	0.000
74	A	1344	LEU	0	-0.090	-0.040	102.876	0.000	0.000	0.000	0.000	0.000	0.000
75	A	1345	MET	0	0.013	0.005	102.087	0.000	0.000	0.000	0.000	0.000	0.000
76	A	1346	GLU	-1	-1.002	-0.980	105.815	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1271:LEU)